Next thing I would recommend is to do the following: With the board powered, press the erase button and after a second, press also the reset button. Keep them pressed for another second. Then power cycle the board and try again the bossac. Good luck!

I learned from this forum that it is mandatory to have the memory erased to make the Bossac bootloader run. In the case of the Arduino, the Due executes a soft erase command when the IDE opens and closes the COM port. May be someone here have grasp more details on this matter.

+ Programming port: To use this port, select "Arduino Due (Programming Port)" as your board in the Arduino IDE. Connect the Due's programming port (the one closest to the DC power jack) to your computer. The programming port uses the 16U2 as a USB-to-serial chip connected to the first UART of the SAM3X (RX0 and TX0). The 16U2 has two pins connected to the Reset and Erase pins of the SAM3X. Opening and closing the Programming port connected at 1200bps triggers a "hard erase" procedure of the SAM3X chip, activating the Erase and Reset pins on the SAM3X before communicating with the UART. This is the recommended port for programming the Due. It is more reliable than the "soft erase" that occurs on the Native port, and it should work even if the main MCU has crashed.